With more than one million page views and more than 4,000 items, this blog provides news and commentary on public policy, business and economic issues related to the $3 billion California stem cell agency, officially known as the California Institute for Regenerative Medicine(CIRM). David Jensen, a retired California newsman, has published this blog since January 2005. His email address is djensen@californiastemcellreport.com.

Wednesday, October 10, 2012

More than one back story exists on
Shinya Yamanaka and his Nobel Prize, but one that has received little
attention this week also raises questions about hoary practice of
peer review and publication of research – not to mention the
awarding of billions of dollars in taxpayer dollars.

The Yamanaka tale goes back to a 2010
article in the New Scientist magazine by Peter Aldous in which the
publication examined more than 200 stem cell papers published from
“2006 onwards.” The study showed an apparent favoritism towards
U.S. scientists. Also specifically reported were long delays in
publication of Yamanaka's papers, including in one case 295 days.

Here is part of what Aldous wrote,

“All's fair in love and war, they
say, but science is supposed to obey more noble ideals. New findings
are submitted for publication, the studies are farmed out to experts
for objective 'peer review' and the best research appears promptly
in the most prestigious journals.

“Some stem cell biologists are crying
foul, however. Last year(2009), 14 researchers in this notoriously
competitive field wrote
to leading journals complaining of "unreasonable or
obstructive reviews". The result, they claimed, is that
'publication of truly original findings may be delayed or rejected.'

“Triggered by this protest, New
Scientist scrutinised the dynamics of publication in the most
exciting and competitive area of stem
cell research, in which cells are 'reprogrammed' to
acquire the versatility of those of an early-stage embryo. In this
fast-moving field, where a Nobel prize is arguably at stake,
biologists are racing feverishly to publish their findings in top
journals.

“Our analysis of more than 200
research papers from 2006 onwards reveals that US-based scientists
are enjoying a significant advantage, getting their papers published
faster and in more prominent journals (find
our data, methods and analyses here).

“More mysterious, given his standing
in the field, is why two of Yamanaka's papers were among the 10 with
the longest lags. In the most delayed of all, Yamanaka reported that
the tumour-suppressing gene p53 inhibits the formation of
iPS cells. The paper took 295 days to be accepted. It was eventually
published by Nature in August 2009 alongside four similar
studies. 'Yamanaka's paper was submitted months before any of the
others,' complains Austin
Smith at the University of Cambridge, UK, who coordinated
the letter sent to leading journals.

“Yamanaka suggests that editors may
be less excited by papers from non-US scientists, but may change
their minds when they receive similar work from leading labs in the
US. In this case, Hochedlinger submitted a paper similar to
Yamanaka's, but nearly six months after him. Ritu
Dhand, Nature's chief biology editor, says that each paper
is assessed on its own merits. Hochedlinger says he was unaware of
Yamanaka's research on p53 before publication.”

Last week, Paul Knoepfler of UC Davis
wrote of other issues dealing with peer review, but coincidentally
also dealing with iPS cells. What New Scientist and Knoepfler are
discussing is not an isolated situation. It is part of a continuum of
complaints, both serious and self-interested but exceedingly
pervasive. A Google search today on the term “problems with peer
review” turned up 10.1 million references. Writing on Ars Technica last year, Jonathan Gitlin, science policy analyst at the National
Human Genome Research Institute,summarized many of the issues, citing a “published” (our quotation marks)
study that said peer review doesn't work “any better than chance.”
Gitlin said,

“A common criticism is that peer
review is biased towards well-established research groups and the
scientific status quo. Reviewers are unwilling to reject papers from
big names in their fields out of fear, and they can be hostile to
ideas that challenge their own, even if the supporting data is good.
Unscrupulous reviewers can reject papers and then quickly publish
similar work themselves.”

At the $3 billion California stem cell
agency, peer review is undergoing some modest, indirect examination
nowadays. The agency is moving towards tighter scrutiny of budgets
proposed by applicants. And, following a record wave of appeals this
summer by disgruntled applicants rejected during peer review, it is
also moving to bring the appeal process under more control.

As the agency tries to move faster and
more successfully towards development of commercial therapies, it may
do well to consider also the frailties of its peer review process and the
perils of scientific orthodoxy.

What is strange about the New Scientist article is it implies that the reason it took over 200 days for Yamanaka to get his paper p53 published in Nature is that Nature has a bias against non-US scientists. However in the data provided in the table, it shows Nature has virtually no bias against non-US scientists in terms of speed of acceptance and publication if reprogramming papers. Seems rather contradictory and unscholarly of Aldhous-- using anecdotal data to bolster his claim of unfairness by Nature, even when it is not supported by the more rigorous approach presented in the tables.

About Me

The California Stem Cell Report is the only nongovernmental website devoted solely to the $3 billion California stem cell agency. The report is published by David Jensen, who worked for 22 years for The Sacramento Bee in a variety of editing positions, including executive business editor and special projects editor. He was the primary editor on the 1992 Pulitzer Prize-winning series, "The Monkey Wars" by Deborah Blum, which dealt with opposition to research on primates. Jensen served as a press aide in the 1974 campaign and first administration of Gov. Jerry Brown. (Time served: two years and one week.) He writes from his sailboat on the west coast of Mexico with occasional visits to land. Jensen began writing about the stem cell agency in 2005, noting that it is an unprecedented effort that uniquely combines big science, big business, big academia, big politics, religion, ethics and morality as well as life and death. The California Stem Cell Report has been identified as one of the best stem cell sites on the Internet. Its readership includes the media (both mainstream and science), a wide range of academic/research institutions globally, the NIH and California policy makers.